[maker-devel] Training Augustus

[Carson Holt]

If your using the maker2zff script you can take MAKER results. And filter them.  This produces ZFF.  Then follow the training steps mentioned for SNAP (removing any obvious errors).  Then use this script to convert the ZFF used for SNAP training to an Augustus training file —> https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl <https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl>

Another thread with more info —> http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html <http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html>

—Carson



> On May 27, 2015, at 4:57 PM, John Cornelius <jcornel3 at asu.edu> wrote:
> 
>  Hi all, I'm trying to train augustus with a non-model organism, I've run Maker, then trained and run SNAP twice and would now like to run Augustus on the results as well. I've seen the Augustus page on training the program and it mentioned needing a list of 200+ quality gene structures for training, is there a way that I could filter the SNAP results for the highest quality genes to feed into augustus? Thanks.
> 
> -- 
> John Cornelius
> MCB PhD Candidate
> Arizona State University
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